Extracts Survey data from Database

Usage

get_survdat_data(
  channel,
  filterByYear = NA,
  all.season = F,
  shg.check = T,
  conversion.factor = T,
  use.SAD = F,
  getBio = F,
  getLengths = T,
  getWeightLength = F
)

Arguments

channel

an Object inherited from DBIConnection-class. This object is used to communicate with the database engine. (see connect_to_database)

filterByYear

Numeric vector. Subset of years from which to pull data. If not specified then all years are pulled. (Default = NA)

all.season

Boolean. Spring and Fall only (F) otherwise T. (Default = F)

shg.check

Boolean. use only SHG <=136 or TOGA <= 1324 (>2008). (Default = T)

conversion.factor

Boolean. Whether to apply conversion factors to the data pull, (Default = T)

use.SAD

Boolean. Use Survey Analysis Database (SAD) for assessed species. (Default = F)

getBio

Boolean. Include biology data for each fish weight, sex, stomach weight, stomach volume, age, maturity

getLengths

Boolean. Include length data which includes the length in cm and the number at length. (Default = T)

getWeightLength

Boolean. Include the weight at length by applying length weight coefficients from SVDBS. (Default = F)

Value

A list containing a Data frame (data.table) (n x 21), a list of SQL queries used to pull the data, the date of the pull, and the call expression. Each row of the data.table represents the number at length of a species on a specific tow along with physical attributes of the tow.

The data frame (Descriptions taken from NEFSC Data dictionary)

CRUISE6

Code uniquely identifying cruise. The first four digits indicate the year and the last two digit uniquely identify the cruise within the year. The 5th byte signifies cruises other than groundfish: Shrimp survey = 7 (i.e. 201470), State of Massachusetts survey = 9 (i.e. 201491), Food habits = 5 (i.e.199554)

STATION

Unique sequential order in which stations have been completed. Hangups and short tows each receive a non-repeated consecutive number.

STRATUM

A predefined area where a net dredge, or other piece of gear was deployed. Code consists of 2 parts: Stratum group code number (2 bytes) and stratum number (3 bytes). Stratum group refers to if area fished is inshore or offshore North or South of Cape Hatteras or the type of cruise (shellfish, State of MA, offshore deepwater). The stratum number (third and fourth digits of code) refers to area defined by depth zone. See SVDBS.SVMSTRATA. The fifth digit of the code increases the length of the stratum number for revised strata after the Hague Line was established. Stratum group code: 01 = Trawl, offshore north of Hatteras; 02 = BIOM; 03 = Trawl, inshore north of Hatteras; 04 = Shrimp; 05 = Scotian shelf; 06 = Shellfish; 07 = Trawl, inshore south of Hatteras; 08 = Trawl, Offshore south of Hatteras; 09 = MA DMF; 99 = Offshore deepwater (outside the stratified area). A change in Bottom Trawl Stratum for the Gulf of Maine-Bay of Fundy has been in effect since Spring 1987, and may be summarized as follows: Previous strata: 01350; Present strata: 01351, 01352.

TOW

Sequential number representing order in which station was selected within a stratum.

SVSPP

A standard code which represents a species caught in a trawl or dredge. Refer to the SVDBS.SVSPECIES_LIST

CATCHSEX

Code used to identify species that are sexed at the catch level. See SVDBS.SEX_CODES

SVVESSEL

Standard two character code for a survey vessel. Refer to SVDBS.SV_VESSEL

YEAR

Year in which cruise was conducted.

SEASON

Season of the year in which cruise was conducted.

LAT

Beginning latitude of tow in decimal degrees.(DECDEG_BEGLAT)

LON

Beginning longitude of tow in decimal degrees.(DECDEG_BEGLON)

EST_TOWDATE

Date and time represented by Eastern Standard Time (EST) for the start of a tow or deployment.(BEGIN_EST_TOWDATE)

DEPTH

A four digit number recording the average depth, to the nearest meter, during a survey gear deployment.(AVGDEPTH)

SURFTEMP

Surface temperature of water (degrees Celcius).

SURFSALIN

Salinity at water surface in practical salinity units (PSU).

BOTTEMP

Bottom temperature (degrees Celsius).

BOTSALIN

Bottom salinity in Practical Salinity Units (PSU).

ABUNDANCE

Expanded number of individuals of a species caught at a given station.(EXPCATCHNUM)

BIOMASS

Expanded catch weight of a species caught at a given station. (EXPCATCHWT)

Additional Columns if getLengths = T (UNION_FSCS_SVLEN)

LENGTH

Measured length of species in centimeters (cm). Measure method differs by species.

NUMLEN

Expanded number of specimens at a given length.(EXPNUMLEN)

Additional Columns if getWeightLength = T

PREDWT

Predicted weight given length based on length-weight coefficients.

WGTLEN

Predicted total weight given number of fish observed at given length

Additional columns if bio = T (UNION_FSCS_SVBIO)

INDID

A unique identifier for each fish sampled.

INDWT

Individual weight (KG) of species being sampled.

SEX

Code indicating sex of fish or invertebrate species. See SVDBS.FSCS_SEX_CODES if using fscs data and SVDBS.SEX_CODES if using non FSCS data. Codes 0, 1, 2 and 4 are the only valid codes in fscs tables.

MATURITY

Stage of maturation of the fish being sampled. See SVDBS.FSCS_MATURITY_CODES

AGE

Age of specimen in years.

STOM_VOLUME

Volume of the stomach contents of the fish sampled, measured to the nearest tenth of a cubic centimeter (cc).

STOM_WGT

Stomach weight of an individual fish in grams.

The list of sql statements:

cruise

Select unique list of cruises. Table = MSTR_CRUISE

station

Select unique set of stations from result of cruise. Table = UNION_FSCS_SVSTA

catch

Select species abundance and biomass data from result of station. Table = UNION_FSCS_SVCAT

length

Select Lengths of species found in catch. Table = UNION_FSCS_SVLEN

sad

Select ????? from Survey Analysis Database. Table = STOCKEFF.I_SV_MERGED_CATCH_CALIB_O

conversions

Select conversion factors. Table = SURVAN_CONVERSION_FACTORS

bio

Select bio stats. Table = UNION_FSCS_SVBIO

The date:

pullDate

The date the data was pulled from the database

The expression:

functionCall

The call used to create the data pull

The version:

version

The version of survdat used to pull the data

See also

Examples

if (FALSE) { # \dontrun{
# First create a connection object to the database
channel <- dbutils::connect_to_database("serverName","userName")
# pull survey data, applies conversion factors (Door, net, vessel) and join with
# biological data to return individual sex, age, maturity, stomach data
get_survdat_data(channel,conversion.factor = T, bio=T)

# Same data pull without individual biological data
get_survdat_data(channel,conversion.factor = T, bio=F)
} # }